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Chaste - Publications

Generic publications

• J. Pitt-Francis, P. Pathmanathan, M.O. Bernabeu, R. Bordas, J. Cooper, A.G. Fletcher, G.R. Mirams, P. Murray, J.M. Osbourne, A. Walter, S.J. Chapman, A. Garny, I.M.M. van Leeuwen, P.K. Maini, B. Rodriguez, S.L. Waters, J.P. Whiteley, H.M. Byrne, D.J. Gavaghan. Chaste: a test-driven approach to software development for biological modelling. Comp Phys Comm 180:2452-2471, 2009. doi: 10.1016/j.cpc.2009.07.019.

Cardiac publications

Electro-physiology

2011

• S. Niederer et al. Verification of cardiac tissue electrophysiology simulators using an N-version benchmark. Royal Society Philosophical Transactions A, 369(1954):4331-4351, 2011. doi: 10.1098/rsta.2011.0139. [Note: this paper compares the accuracy of various cardiac electro-physiology solvers, including Chaste].
• P. Pathmanathan, M. Bernabeu, S. Niederer, D. Gavaghan, D. Kay. Computational modelling of cardiac electro-physiology: explanation of the variability of results from different numerical solvers. J. Numerical Methods in Biomedical Engineering (accepted for publication) , 2011. (Local pre-print)
• J. Cooper, G. Mirams, S. Niederer. High throughput functional curation of cellular electrophysiology models. Prog Biophys Mol Biol, 2011. doi: 10.1016/j.pbiomolbio.2011.06.003. (Local pre-print)
• G.R. Mirams, Y. Cui, A. Sher, M. Fink, J. Cooper, B.M. Heath, N.C. McMahon, D.J. Gavaghan, D. Noble. Simulation of multiple ion channel block provides improved early prediction of compounds' clinical torsadogenic risk. Cardiovascular Research, (online ahead of print) 2011. doi: 10.1093/cvr/CVR044
• P. Pathmanathan, G.R. Mirams, J. Southern, J.P. Whiteley. The significant effect of the choice of ionic current integration method in cardiac electro-physiological simulations. International Journal for Numerical Methods in Biomedical Engineering , (online ahead of print), 2011. doi:10.1002/cnm.1438

2010

• M.O. Bernabeu, P. Pathmanathan, J.M. Pitt-Francis, D. Kay. Stimulus protocol determines the most computationally-efficient preconditioner for the bidomain equations. IEEE Transactions in Biomedical Engineering , 57(12):2806-2815, 2010. doi:10.1109/TBME.2010.2078817
• P. Pathmanathan, M.O. Bernabeu, R. Bordas, J. Cooper, A. Garny, J.M. Pitt-Francis, J.P. Whiteley and D.J. Gavaghan. A numerical guide to the solution of the bidomain equations of cardiac electrophysiology. Progress in Biophysics and Molecular Biology, 102(2-3):136-155, 2010. doi: 10.1016/j.pbiomolbio.2010.05.006
• C. Sanchez, A. Corrias, P. Laguna, E. Pueyo and B. Rodriguez. Sensitivity of atrial fibrillation related biomarkers to changes in ionic current properties. Heart Rhythm, 2010. (Abstract)
• A. Corrias, E. Pueyo, K. Burrage and B. Rodriguez. Causes of variability in ventricular repolarization: from isolated cells to ECG. Heart Rhythm, 2010. (Abstract)
• David Abramson, Miguel O. Bernabeu, Blair Bethwaite, Kevin Burrage, Alberto Corrias, Colin Enticott, Slavisa Garic, David Gavaghan, Tom Peachey, J. Pitt-Francis, E. Pueyo, Blanca Rodriguez, Anna Sher and Jefferson Tan. High-throughput cardiac science on the Grid. Phil. Trans. R. Soc. A 368(1925):3907-3923, 2010. doi: 10.1098/rsta.2010.0170
• J. Southern, G.J. Gorman, M.D. Piggott, P.E. Farrell, M.O. Bernabeu and J. Pitt-Francis. Simulating cardiac electrophysiology using anisotropic mesh adaptivity. Journal of Computational Science 1(2):82-88, 2010. doi: 10.1016/j.jocs.2010.03.010.
• A. Corrias, X. Jie, L. Romero, M.J. Bishop, M. Bernabeu, E. Pueyo, B. Rodriguez. Arrhythmic risk biomarkers for the assessment of drug cardiotoxicity: from experiments to computer simulations. Phil Trans Roy Soc A 368(1921):3001-3025, 2010. doi: 10.1098/rsta.2010.0083

2009

• M.O. Bernabeu, R. Bordas, P. Pathmanathan, J. Pitt-Francis, J. Cooper, A. Garny, D.J. Gavaghan, B. Rodriguez, J.A. Southern, J.P. Whiteley. Chaste: Incorporating a novel multi-scale spatial and temporal algorithm into a large-scale open-source library. Phil Trans Roy Soc A 367(1895):1907-1930, 2009. doi: 10.1098/rsta.2008.0309.

2008

• M.O. Bernabeu, M.J. Bishop, J. Pitt-Francis, D.J. Gavaghan, V. Grau and B. Rodriguez. High performance computer study of biological function in 3D heart models incorporating fibre orientation and realistic geometry at para-cellular resolution. Computers in Cardiology, 2008, pp721-724. doi: 10.1109/CIC.2008.4749143.
• J. Pitt-Francis, M.O. Bernabeu, J. Cooper, A. Garny, L. Momtahan, J. Osborne, P. Pathmanathan, B. Rodriguez, J.P. Whiteley and D.J. Gavaghan. Chaste: Using agile programming techniques to develop computational biology software. Phil Trans Roy Soc A 366(1878):3111-3136, 2008. doi: 10.1098/rsta.2008.0096.

Electro-mechanics

• P. Pathmanathan, S.J. Chapman, D.J. Gavaghan and J.P. Whiteley. Cardiac electromechanics: the effect of contraction model on the mathematical problem and accuracy of the numerical scheme. Quarterly Journal of Mechanics and Applied Mathematics 63(3):375-399, 2010. doi: 10.1093/qjmam/hbq014.
• P. Pathmanathan and J.P. Whiteley. A numerical method for cardiac mechanoelectric simulations. Ann Biomed Eng 37(5):860-873, 2009. doi: 10.1007/s10439-009-9663-8.

PyCml

• J. Cooper, A. Corrias, D. Gavaghan, D. Noble. Considerations for the use of cellular electrophysiology models within cardiac tissue simulations. Prog Biophys Mol Biol, 2011. doi: 10.1016/j.pbiomolbio.2011.06.002. (Local pre-print)
• J. Cooper. Automatic Validation and Optimisation of Biological Models. DPhil Thesis, University of Oxford, 2009. ORA record. (Local copy)
• J. Cooper, S. McKeever. A model-driven approach to automatic conversion of physical units. Softw Pract Exper 38(4):337-359, 2008. doi: 10.1002/spe.828.
• J. Cooper, S. McKeever, A.Garny. On the application of partial evaluation to the optimisation of cardiac electrophysiological simulations. In PEPM '06: Proceedings of the 2006 ACM SIGPLAN symposium on Partial evaluation and semantics-based program manipulation 12-20, 2006. doi: 10.1145/1111542.1111546.

Cell-based publications

• A.G. Fletcher, C.J. Breward and S.J. Chapman. Mathematical modelling of monoclonal conversion in the colonic crypt. J Theor Biol 300:118-133, 2012. doi:10.1016/j.jtbi.2012.01.021.
• S.-J. Dunn, A.G. Fletcher, S.J. Chapman, D.J. Gavaghan, J.M. Osborne. Modelling the role of the basement membrane in the colonic epithelium. J Theor Biol 298:82-91, 2012. doi:10.1016/j.jtbi.2011.12.013.
• A.G. Fletcher, G.R. Mirams, P.J. Murray, A. Walter, J.-W. Kang, K.-H. Cho, P.K. Maini and H.M. Byrne. Multiscale modeling of colonic crypts and early colorectal cancer. In T.S. Deisboeck and G. Stamatakos (eds) Multiscale Cancer Modeling 111-134, CRC Press, 2010. ISBN: 9781439814406.
• J.M. Osborne, A. Walter, S.K. Kershaw, G.R. Mirams, A.G. Fletcher, P. Pathmanathan, D.J. Gavaghan, O.E. Jensen, P.K. Maini and H.M. Byrne. A hybrid approach to multiscale modelling of cancer. Phil Trans Roy Soc A 368:5013-5028, 2010. doi: 10.1098/rsta.2010.0173.
• P. Pathmanathan, J. Cooper, A. Fletcher, G. Mirams, P. Murray, J. Osborne, J. Pitt-Francis, A. Walter and S.J. Chapman. A computational study of discrete mechanical tissue models. Phys Biol 6:036001, 2009. doi: 10.1088/1478-3975/6/3/036001.
• I.M.M. van Leeuwen, G.R. Mirams, A. Walter, A. Fletcher, P. Murray, J. Osborne, S. Varma, S.J. Young, J. Cooper, J. Pitt-Francis, L. Momtahan, P. Pathmanathan, J.P. Whiteley, S.J. Chapman, D.J. Gavaghan, O.E. Jensen, J.R. King, P.K. Maini, S.L. Waters and H.M. Byrne. An integrative computational model for intestinal tissue renewal. Cell Prolif 42:617-636, 2009. doi: 10.1111/j.1365-2184.2009.00627.x.